libpappsomspp
Library for mass spectrometry
pappso::TimsMsRunReaderMs2 Class Reference

#include <timsmsrunreaderms2.h>

Inheritance diagram for pappso::TimsMsRunReaderMs2:
pappso::MsRunReader pappso::TimsMsRunReaderMs2Selected

Public Member Functions

 TimsMsRunReaderMs2 (MsRunIdCstSPtr &msrun_id_csp)
 
virtual ~TimsMsRunReaderMs2 ()
 
virtual MassSpectrumSPtr massSpectrumSPtr (std::size_t spectrum_index) override
 get a MassSpectrumSPtr class given its spectrum index More...
 
virtual MassSpectrumCstSPtr massSpectrumCstSPtr (std::size_t spectrum_index) override
 
virtual QualifiedMassSpectrum qualifiedMassSpectrum (std::size_t spectrum_index, bool want_binary_data=true) const override
 get a QualifiedMassSpectrum class given its scan number More...
 
virtual void readSpectrumCollection (SpectrumCollectionHandlerInterface &handler) override
 function to visit an MsRunReader and get each Spectrum in a spectrum collection handler More...
 
virtual pappso::XicCoordSPtr newXicCoordSPtrFromSpectrumIndex (std::size_t spectrum_index, pappso::PrecisionPtr precision) const override
 get a xic coordinate object from a given spectrum index More...
 
virtual pappso::XicCoordSPtr newXicCoordSPtrFromQualifiedMassSpectrum (const pappso::QualifiedMassSpectrum &mass_spectrum, pappso::PrecisionPtr precision) const override
 get a xic coordinate object from a given spectrum More...
 
virtual void readSpectrumCollectionByMsLevel (SpectrumCollectionHandlerInterface &handler, unsigned int ms_level) override
 function to visit an MsRunReader and get each Spectrum in a spectrum collection handler by Ms Levels More...
 
virtual std::size_t spectrumListSize () const override
 get the totat number of spectrum conained in the MSrun data file More...
 
virtual bool hasScanNumbers () const override
 tells if spectra can be accessed using scan numbers by default, it returns false. Only overrided functions can check if scan numbers are available in the current file More...
 
void setMs2FilterCstSPtr (pappso::FilterInterfaceCstSPtr filter)
 
void setMs1FilterCstSPtr (pappso::FilterInterfaceCstSPtr filter)
 
void setMs2BuiltinCentroid (bool centroid)
 enable or disable simple centroid filter on raw tims data for MS2 More...
 
virtual std::vector< std::size_t > getPrecursorsIDFromMzRt (int charge, double mz_val, double rt_sec, double k0)
 Get all the precursors id which match the values. More...
 
virtual bool releaseDevice () override
 release data back end device if a the data back end is released, the developper has to use acquireDevice before using the msrunreader object More...
 
virtual bool acquireDevice () override
 acquire data back end device More...
 
virtual TimsDataSp getTimsDataSPtr ()
 give an access to the underlying raw data pointer More...
 
virtual std::vector< double > getRetentionTimeLine () override
 retention timeline get retention times along the MSrun in seconds More...
 
virtual Trace getTicChromatogram () override
 
- Public Member Functions inherited from pappso::MsRunReader
 MsRunReader (MsRunIdCstSPtr &ms_run_id)
 
 MsRunReader (const MsRunReader &other)
 
virtual ~MsRunReader ()
 
const MsRunIdCstSPtrgetMsRunId () const
 
virtual std::size_t scanNumber2SpectrumIndex (std::size_t scan_number)
 if possible, converts a scan number into a spectrum index This is a convenient function to help transition from the old scan number (not implemented by all vendors) to more secure spectrum index (not vendor dependant). It is better to not rely on this function. More...
 

Protected Member Functions

virtual void initialize () override
 
virtual bool accept (const QString &file_name) const override
 tells if the reader is able to handle this file must be implemented by private MS run reader, specific of one or more file format More...
 

Private Attributes

TimsDataSp msp_timsData = nullptr
 
pappso::FilterInterfaceCstSPtr msp_ms1Filter
 
pappso::FilterInterfaceCstSPtr msp_ms2Filter
 
bool m_builtinMs2Centroid = true
 enable builtin centroid on raw tims integers by default More...
 

Friends

class MsFileAccessor
 

Additional Inherited Members

- Protected Attributes inherited from pappso::MsRunReader
MsRunIdCstSPtr mcsp_msRunId
 
MsRunReaderScanNumberMultiMapmpa_multiMapScanNumber = nullptr
 

Detailed Description

Definition at line 40 of file timsmsrunreaderms2.h.

Constructor & Destructor Documentation

◆ TimsMsRunReaderMs2()

TimsMsRunReaderMs2::TimsMsRunReaderMs2 ( MsRunIdCstSPtr msrun_id_csp)
Todo:
write docs

Definition at line 39 of file timsmsrunreaderms2.cpp.

40  : MsRunReader(msrun_id_csp)
41 {
42  initialize();
43 }
MsRunReader(MsRunIdCstSPtr &ms_run_id)
virtual void initialize() override

References initialize().

◆ ~TimsMsRunReaderMs2()

TimsMsRunReaderMs2::~TimsMsRunReaderMs2 ( )
virtual

Definition at line 45 of file timsmsrunreaderms2.cpp.

46 {
47  if(msp_timsData != nullptr)
48  {
49  msp_timsData = nullptr;
50  }
51 }

References msp_timsData.

Member Function Documentation

◆ accept()

bool TimsMsRunReaderMs2::accept ( const QString &  file_name) const
overrideprotectedvirtual

tells if the reader is able to handle this file must be implemented by private MS run reader, specific of one or more file format

Implements pappso::MsRunReader.

Reimplemented in pappso::TimsMsRunReaderMs2Selected.

Definition at line 116 of file timsmsrunreaderms2.cpp.

117 {
118  qDebug() << file_name;
119  return true;
120 }

◆ acquireDevice()

bool TimsMsRunReaderMs2::acquireDevice ( )
overridevirtual

acquire data back end device

Returns
bool true if done

Implements pappso::MsRunReader.

Definition at line 255 of file timsmsrunreaderms2.cpp.

256 {
257  if(msp_timsData == nullptr)
258  {
259  initialize();
260  msp_timsData->setMs2BuiltinCentroid(m_builtinMs2Centroid);
261  msp_timsData->setMs1FilterCstSPtr(msp_ms1Filter);
262  msp_timsData->setMs2FilterCstSPtr(msp_ms2Filter);
263  }
264  return true;
265 }
pappso::FilterInterfaceCstSPtr msp_ms2Filter
pappso::FilterInterfaceCstSPtr msp_ms1Filter
bool m_builtinMs2Centroid
enable builtin centroid on raw tims integers by default

References initialize(), m_builtinMs2Centroid, msp_ms1Filter, msp_ms2Filter, and msp_timsData.

Referenced by getTicChromatogram().

◆ getPrecursorsIDFromMzRt()

std::vector< std::size_t > pappso::TimsMsRunReaderMs2::getPrecursorsIDFromMzRt ( int  charge,
double  mz_val,
double  rt_sec,
double  k0 
)
virtual

Get all the precursors id which match the values.

Returns
list of precursors Ids

Definition at line 268 of file timsmsrunreaderms2.cpp.

272 {
273  return msp_timsData->getPrecursorsFromMzRtCharge(charge, mz_val, rt_sec, k0);
274 }

◆ getRetentionTimeLine()

std::vector< double > pappso::TimsMsRunReaderMs2::getRetentionTimeLine ( )
overridevirtual

retention timeline get retention times along the MSrun in seconds

Returns
vector of retention times (seconds)

Reimplemented from pappso::MsRunReader.

Definition at line 312 of file timsmsrunreaderms2.cpp.

313 {
314  return msp_timsData.get()->getRetentionTimeLine();
315 }

◆ getTicChromatogram()

Trace TimsMsRunReaderMs2::getTicChromatogram ( )
overridevirtual

Reimplemented from pappso::MsRunReader.

Definition at line 318 of file timsmsrunreaderms2.cpp.

319 {
320  // Use the Sqlite database to fetch the total ion current chromatogram (TIC
321  // chromatogram).
322 
323  acquireDevice();
324 
325  return msp_timsData->getTicChromatogram();
326 }
virtual bool acquireDevice() override
acquire data back end device

References acquireDevice(), and msp_timsData.

◆ getTimsDataSPtr()

pappso::TimsDataSp pappso::TimsMsRunReaderMs2::getTimsDataSPtr ( )
virtual

give an access to the underlying raw data pointer

Definition at line 277 of file timsmsrunreaderms2.cpp.

278 {
279  acquireDevice();
280  return msp_timsData;
281 }

Referenced by pappso::TimsXicExtractorInterface::TimsXicExtractorInterface().

◆ hasScanNumbers()

bool TimsMsRunReaderMs2::hasScanNumbers ( ) const
overridevirtual

tells if spectra can be accessed using scan numbers by default, it returns false. Only overrided functions can check if scan numbers are available in the current file

Reimplemented from pappso::MsRunReader.

Reimplemented in pappso::TimsMsRunReaderMs2Selected.

Definition at line 241 of file timsmsrunreaderms2.cpp.

242 {
243  return false;
244 }

◆ initialize()

void pappso::TimsMsRunReaderMs2::initialize ( )
overrideprotectedvirtual

Implements pappso::MsRunReader.

Reimplemented in pappso::TimsMsRunReaderMs2Selected.

Definition at line 54 of file timsmsrunreaderms2.cpp.

55 {
56  msp_timsData = std::make_shared<TimsData>(mcsp_msRunId.get()->getFileName());
57  if(msp_timsData == nullptr)
58  {
59  throw PappsoException(
60  QObject::tr("ERROR in TimsMsRunReaderMs2::initialize "
61  "msp_timsData is null for MsRunId %1")
62  .arg(mcsp_msRunId.get()->toString()));
63  }
64 
65 }
MsRunIdCstSPtr mcsp_msRunId
Definition: msrunreader.h:282

Referenced by TimsMsRunReaderMs2(), and acquireDevice().

◆ massSpectrumCstSPtr()

pappso::MassSpectrumCstSPtr TimsMsRunReaderMs2::massSpectrumCstSPtr ( std::size_t  spectrum_index)
overridevirtual

Implements pappso::MsRunReader.

Reimplemented in pappso::TimsMsRunReaderMs2Selected.

Definition at line 133 of file timsmsrunreaderms2.cpp.

134 {
135  QualifiedMassSpectrum mass_spectrum =
136  qualifiedMassSpectrum(spectrum_index, true);
137  return mass_spectrum.getMassSpectrumSPtr();
138 }
Class representing a fully specified mass spectrum.
MassSpectrumSPtr getMassSpectrumSPtr() const
Get the MassSpectrumSPtr.
virtual QualifiedMassSpectrum qualifiedMassSpectrum(std::size_t spectrum_index, bool want_binary_data=true) const override
get a QualifiedMassSpectrum class given its scan number

References pappso::QualifiedMassSpectrum::getMassSpectrumSPtr(), and qualifiedMassSpectrum().

◆ massSpectrumSPtr()

pappso::MassSpectrumSPtr TimsMsRunReaderMs2::massSpectrumSPtr ( std::size_t  spectrum_index)
overridevirtual

get a MassSpectrumSPtr class given its spectrum index

Implements pappso::MsRunReader.

Reimplemented in pappso::TimsMsRunReaderMs2Selected.

Definition at line 124 of file timsmsrunreaderms2.cpp.

125 {
126  QualifiedMassSpectrum mass_spectrum =
127  qualifiedMassSpectrum(spectrum_index, true);
128  return mass_spectrum.getMassSpectrumSPtr();
129 }

References pappso::QualifiedMassSpectrum::getMassSpectrumSPtr(), and qualifiedMassSpectrum().

◆ newXicCoordSPtrFromQualifiedMassSpectrum()

pappso::XicCoordSPtr TimsMsRunReaderMs2::newXicCoordSPtrFromQualifiedMassSpectrum ( const pappso::QualifiedMassSpectrum mass_spectrum,
pappso::PrecisionPtr  precision 
) const
overridevirtual

get a xic coordinate object from a given spectrum

Implements pappso::MsRunReader.

Definition at line 303 of file timsmsrunreaderms2.cpp.

306 {
308  mass_spectrum.getMassSpectrumId().getSpectrumIndex(), precision);
309 }
std::size_t getSpectrumIndex() const
const MassSpectrumId & getMassSpectrumId() const
Get the MassSpectrumId.
virtual pappso::XicCoordSPtr newXicCoordSPtrFromSpectrumIndex(std::size_t spectrum_index, pappso::PrecisionPtr precision) const override
get a xic coordinate object from a given spectrum index

References pappso::QualifiedMassSpectrum::getMassSpectrumId(), pappso::MassSpectrumId::getSpectrumIndex(), and newXicCoordSPtrFromSpectrumIndex().

◆ newXicCoordSPtrFromSpectrumIndex()

XicCoordSPtr TimsMsRunReaderMs2::newXicCoordSPtrFromSpectrumIndex ( std::size_t  spectrum_index,
pappso::PrecisionPtr  precision 
) const
overridevirtual

get a xic coordinate object from a given spectrum index

Implements pappso::MsRunReader.

Definition at line 285 of file timsmsrunreaderms2.cpp.

287 {
288  XicCoordTimsSPtr xic_coord = std::make_shared<XicCoordTims>();
289  std::size_t precursor_index = (spectrum_index / 2) + 1;
290  auto xic = this->msp_timsData.get()->getXicCoordTimsFromPrecursorId(
291  precursor_index, precision);
292 
293  xic_coord.get()->mzRange = xic.mzRange;
294  xic_coord.get()->rtTarget = xic.rtTarget;
295  xic_coord.get()->scanNumBegin = xic.scanNumBegin;
296  xic_coord.get()->scanNumEnd = xic.scanNumEnd;
297 
298 
299  return xic_coord;
300 }
std::shared_ptr< XicCoordTims > XicCoordTimsSPtr
Definition: xiccoordtims.h:38

References msp_timsData.

Referenced by newXicCoordSPtrFromQualifiedMassSpectrum().

◆ qualifiedMassSpectrum()

QualifiedMassSpectrum TimsMsRunReaderMs2::qualifiedMassSpectrum ( std::size_t  spectrum_index,
bool  want_binary_data = true 
) const
overridevirtual

get a QualifiedMassSpectrum class given its scan number

Implements pappso::MsRunReader.

Reimplemented in pappso::TimsMsRunReaderMs2Selected.

Definition at line 142 of file timsmsrunreaderms2.cpp.

144 {
145 
146  std::size_t precursor_index = (spectrum_index / 2) + 1;
147  TimsData::SpectrumDescr spectrum_descr;
148  try
149  {
150  spectrum_descr =
151  msp_timsData.get()->getSpectrumDescrWithPrecursorId(precursor_index);
152  }
153  catch(ExceptionNotFound &error)
154  {
155  throw ExceptionNotFound(
156  QObject::tr("spectrum_index %1 NOT FOUND in file %2 : %3")
157  .arg(spectrum_index)
158  .arg(getMsRunId().get()->getFileName())
159  .arg(error.qwhat()));
160  }
161 
162  if(spectrum_index % 2 == 0)
163  {
164  qDebug() << "MS1 spectrum precursor_index=" << precursor_index;
165  // this is an MS1 spectrum
166  QualifiedMassSpectrum mass_spectrum_ms1;
167  msp_timsData->getQualifiedMs1MassSpectrumByPrecursorId(
168  getMsRunId(), mass_spectrum_ms1, spectrum_descr, want_binary_data);
169  qDebug(); // << mass_spectrum_ms1.toString();
170 
171  // qDebug() << mass_spectrum_ms1.getMassSpectrumSPtr().get()->toString();
172  return mass_spectrum_ms1;
173  }
174  else
175  {
176  qDebug() << "MS2 spectrum precursor_index=" << precursor_index;
177  QualifiedMassSpectrum mass_spectrum_ms2;
178  if(spectrum_descr.ms2_index != spectrum_index)
179  {
180  qDebug();
181  throw PappsoException(
182  QObject::tr("ERROR in %1 %2 %3 spectrum_descr.ms2_index(%4) != "
183  "spectrum_index(%5)")
184  .arg(__FILE__)
185  .arg(__FUNCTION__)
186  .arg(__LINE__)
187  .arg(spectrum_descr.ms2_index)
188  .arg(spectrum_index));
189  }
190 
191  msp_timsData->getQualifiedMs2MassSpectrumByPrecursorId(
192  getMsRunId(), mass_spectrum_ms2, spectrum_descr, want_binary_data);
193  qDebug(); // << mass_spectrum_ms2.toString();
194 
195  // qDebug() << mass_spectrum_ms2.getMassSpectrumSPtr().get()->toString();
196  return mass_spectrum_ms2;
197  }
198 }
const MsRunIdCstSPtr & getMsRunId() const
virtual const QString & qwhat() const

References pappso::MsRunReader::getMsRunId(), pappso::TimsData::SpectrumDescr::ms2_index, msp_timsData, and pappso::PappsoException::qwhat().

Referenced by massSpectrumCstSPtr(), and massSpectrumSPtr().

◆ readSpectrumCollection()

void TimsMsRunReaderMs2::readSpectrumCollection ( SpectrumCollectionHandlerInterface handler)
overridevirtual

function to visit an MsRunReader and get each Spectrum in a spectrum collection handler

Implements pappso::MsRunReader.

Reimplemented in pappso::TimsMsRunReaderMs2Selected.

Definition at line 202 of file timsmsrunreaderms2.cpp.

204 {
206 }
virtual void readSpectrumCollectionByMsLevel(SpectrumCollectionHandlerInterface &handler, unsigned int ms_level) override
function to visit an MsRunReader and get each Spectrum in a spectrum collection handler by Ms Levels

References readSpectrumCollectionByMsLevel().

◆ readSpectrumCollectionByMsLevel()

void TimsMsRunReaderMs2::readSpectrumCollectionByMsLevel ( SpectrumCollectionHandlerInterface handler,
unsigned int  ms_level 
)
overridevirtual

function to visit an MsRunReader and get each Spectrum in a spectrum collection handler by Ms Levels

Implements pappso::MsRunReader.

Definition at line 209 of file timsmsrunreaderms2.cpp.

211 {
212  qDebug() << " ms_level=" << ms_level;
213  // We'll need it to perform the looping in the spectrum list.
214  std::size_t spectrum_list_size = spectrumListSize();
215 
216  // qDebug() << "The spectrum list has size:" << spectrum_list_size;
217 
218  // Inform the handler of the spectrum list so that it can handle feedback to
219  // the user.
220  handler.spectrumListHasSize(spectrum_list_size);
221 
222  msp_timsData.get()->ms2ReaderSpectrumCollectionByMsLevel(
223  getMsRunId(), handler, ms_level);
224  // Now let the loading handler know that the loading of the data has ended.
225  // The handler might need this "signal" to perform additional tasks or to
226  // cleanup cruft.
227 
228  // qDebug() << "Loading ended";
229  handler.loadingEnded();
230 }
virtual void spectrumListHasSize(std::size_t size)
Definition: msrunreader.cpp:52
virtual std::size_t spectrumListSize() const override
get the totat number of spectrum conained in the MSrun data file

References pappso::MsRunReader::getMsRunId(), pappso::SpectrumCollectionHandlerInterface::loadingEnded(), msp_timsData, pappso::SpectrumCollectionHandlerInterface::spectrumListHasSize(), and spectrumListSize().

Referenced by readSpectrumCollection().

◆ releaseDevice()

bool TimsMsRunReaderMs2::releaseDevice ( )
overridevirtual

release data back end device if a the data back end is released, the developper has to use acquireDevice before using the msrunreader object

Returns
bool true if done

Implements pappso::MsRunReader.

Definition at line 248 of file timsmsrunreaderms2.cpp.

249 {
250  msp_timsData = nullptr;
251  return true;
252 }

References msp_timsData.

◆ setMs1FilterCstSPtr()

void TimsMsRunReaderMs2::setMs1FilterCstSPtr ( pappso::FilterInterfaceCstSPtr  filter)

Definition at line 100 of file timsmsrunreaderms2.cpp.

101 {
102  msp_ms1Filter = filter;
103  if(msp_timsData != nullptr)
104  {
105  msp_timsData->setMs1FilterCstSPtr(filter);
106  }
107  else
108  {
109  throw PappsoException(
110  QObject::tr("ERROR in TimsMsRunReaderMs2::setMs1FilterCstSPtr "
111  "msp_timsData is null"));
112  }
113 }

References msp_ms1Filter, and msp_timsData.

◆ setMs2BuiltinCentroid()

void TimsMsRunReaderMs2::setMs2BuiltinCentroid ( bool  centroid)

enable or disable simple centroid filter on raw tims data for MS2

Definition at line 68 of file timsmsrunreaderms2.cpp.

69 {
70  m_builtinMs2Centroid = centroid;
71  if(msp_timsData != nullptr)
72  {
73  msp_timsData->setMs2BuiltinCentroid(m_builtinMs2Centroid);
74  }
75  else
76  {
77  throw PappsoException(
78  QObject::tr("ERROR in TimsMsRunReaderMs2::setMs2BuiltinCentroid "
79  "msp_timsData is null"));
80  }
81 }

References m_builtinMs2Centroid, and msp_timsData.

Referenced by pappso::TandemWrapperRun::convertOrginalMsData2mzXmlData().

◆ setMs2FilterCstSPtr()

void TimsMsRunReaderMs2::setMs2FilterCstSPtr ( pappso::FilterInterfaceCstSPtr  filter)

Definition at line 84 of file timsmsrunreaderms2.cpp.

85 {
86  msp_ms2Filter = filter;
87  if(msp_timsData != nullptr)
88  {
89  msp_timsData->setMs2FilterCstSPtr(msp_ms2Filter);
90  }
91  else
92  {
93  throw PappsoException(
94  QObject::tr("ERROR in TimsMsRunReaderMs2::setMs2FilterCstSPtr "
95  "msp_timsData is null"));
96  }
97 }

References msp_ms2Filter, and msp_timsData.

Referenced by pappso::TandemWrapperRun::convertOrginalMsData2mzXmlData().

◆ spectrumListSize()

std::size_t TimsMsRunReaderMs2::spectrumListSize ( ) const
overridevirtual

get the totat number of spectrum conained in the MSrun data file

Implements pappso::MsRunReader.

Reimplemented in pappso::TimsMsRunReaderMs2Selected.

Definition at line 234 of file timsmsrunreaderms2.cpp.

235 {
236  return (msp_timsData->getTotalNumberOfPrecursors() * 2);
237 }

References msp_timsData.

Referenced by readSpectrumCollectionByMsLevel().

Friends And Related Function Documentation

◆ MsFileAccessor

friend class MsFileAccessor
friend

Definition at line 42 of file timsmsrunreaderms2.h.

Member Data Documentation

◆ m_builtinMs2Centroid

bool pappso::TimsMsRunReaderMs2::m_builtinMs2Centroid = true
private

enable builtin centroid on raw tims integers by default

Definition at line 121 of file timsmsrunreaderms2.h.

Referenced by acquireDevice(), and setMs2BuiltinCentroid().

◆ msp_ms1Filter

pappso::FilterInterfaceCstSPtr pappso::TimsMsRunReaderMs2::msp_ms1Filter
private

Definition at line 117 of file timsmsrunreaderms2.h.

Referenced by acquireDevice(), and setMs1FilterCstSPtr().

◆ msp_ms2Filter

pappso::FilterInterfaceCstSPtr pappso::TimsMsRunReaderMs2::msp_ms2Filter
private

Definition at line 118 of file timsmsrunreaderms2.h.

Referenced by acquireDevice(), and setMs2FilterCstSPtr().

◆ msp_timsData


The documentation for this class was generated from the following files: